1pz2
From Proteopedia
(Difference between revisions)
| Line 3: | Line 3: | ||
<StructureSection load='1pz2' size='340' side='right'caption='[[1pz2]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='1pz2' size='340' side='right'caption='[[1pz2]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1pz2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1pz2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PZ2 FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene></td></tr> | |
| - | <tr id=' | + | |
| - | + | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz2 OCA], [https://pdbe.org/1pz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pz2 RCSB], [https://www.ebi.ac.uk/pdbsum/1pz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz2 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz2 OCA], [https://pdbe.org/1pz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pz2 RCSB], [https://www.ebi.ac.uk/pdbsum/1pz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz2 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/IABF_GEOSE IABF_GEOSE] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref> <ref>PMID:7887599</ref> | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 22: | Line 20: | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pz2 ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pz2 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis. | ||
| - | |||
| - | Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.,Hovel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D EMBO J. 2003 Oct 1;22(19):4922-32. PMID:14517232<ref>PMID:14517232</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1pz2" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Geobacillus stearothermophilus]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | + | [[Category: Baasov T]] | |
| - | [[Category: Baasov | + | [[Category: Belakhov V]] |
| - | [[Category: Belakhov | + | [[Category: Hoevel K]] |
| - | [[Category: Hoevel | + | [[Category: Niefind K]] |
| - | [[Category: Niefind | + | [[Category: Schomburg D]] |
| - | [[Category: Schomburg | + | [[Category: Shallom D]] |
| - | [[Category: Shallom | + | [[Category: Shoham G]] |
| - | [[Category: Shoham | + | [[Category: Shoham Y]] |
| - | [[Category: Shoham | + | |
| - | + | ||
| - | + | ||
Revision as of 06:00, 17 April 2024
Crystal structure of a transient covalent reaction intermediate of a family 51 alpha-L-arabinofuranosidase
| |||||||||||
